Shami Chakrabarti, the director of Liberty, accused courts of setting a “dangerous” precedent by making “theological” decisions about which faiths deserved protection.

She also warned those who wish to see religion banished from the public square of the “unintended consequences” of people being forced to keep their beliefs private.

Her comments come amid growing tensions between campaigners for anti-discrimination rights and defenders of religious conscience.

Earlier this year peers led by bishops in the House of Lords defeated plans to restrict their employment practices in the Equality Bill, with both the Pope and the Archbishop of Canterbury speaking out against the Government.

Last week five prominent bishops led by the former spiritual head of the Church of England, Lord Carey, warned in a letter to The Sunday Telegraph that Christian beliefs are “simply not being upheld” in this country.

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It follows a string of cases in courts and employment tribunals in which churchgoers who expressed their faith at work were “treated with disrespect”.

Despite being best known as a supporter of the rights of minority groups such as asylum seekers and terrorist suspects, Miss Chakrabarti spoke up on behalf of Britain’s Christian majority in a recent speech on religious rights in the workplace at Queen Mary, University of London.

She highlighted the long-running case of Nadia Eweida, a member of British Airways’ check-in staff who was banned from wearing a visible cross at work. Earlier this year the Court of Appeal ruled that she had not been discriminated against, on the grounds that not all Christians wear symbols of their faith.

Miss Chakrabarti said: “This fundamentally misunderstands the nature of freedom of thought, conscience and belief. Of course it interferes with someone’s right to manifest their religion if you prevent them doing something that they consider to be an expression of their faith.

“The decision also means that tribunals will be required to generalise about religions in order to establish whether there is indirect discrimination. That is exactly the kind of theological adjudication that secular courts are not supposed to do.

“Because Liberty believes the Court of Appeal judgement has set a dangerous precedent we are representing Ms Eweida and we have sought permission to appeal to the Supreme Court.”

She went on: “It seems to me that the Court of Appeal’s judgement has fuel to the fire of those that think or want to think that the law does nothing to protect them. It bends over backwards for Muslims and Sikhs while Christians are being persecuted with impunity.

“This is a deeply divisive narrative which is far more likely to undermine the rights of other religious minority than it is ever to help Christians. If the Supreme Court finds favour in Ms Eweida’s appeal, and I very much hope it will, it has dual benefits of correcting the law and sending a clear message to everyone that is there to protect them as much as any other religious or belief group.”

Miss Chakrabarti said that sometimes employers do have to interfere with the beliefs of staff, such as in the case of Lillian Ladele, the Islington Council registrar who would not carry out civil partnership ceremonies for same-sex couples.

“It would be a nonsense if Islington were obliged to accommodate her belief on the one hand and have a duty not to discriminate on grounds of sexual orientation on the other.”

However she warned against attempts to keep all expressions of religious belief behind closed doors.

“The notion that there is a bright line between private sphere where you can do what you like and the public and work space where you check and important part of your personality at the door can have, I think, dangerous and unintended consequences for everyone.

“Does anyone want a paradigm where a private home or religious place becomes a no-go zone for child protection or other vital law enforcement in some kind of trade off for keeping the public sphere harmoniously vanilla?”

She pointed out: “There is no right not to be irritated or even offended.

“Nobody ever said that life in a rich, diverse democracy would be easy or that the workplace wouldn’t occasionally be a place of tension and strife.”